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estMOI specifications


Unique identifier OMICS_02240
Name estMOI
Software type Application/Script
Interface Command line interface
Restrictions to use None
Input data An alignment, variant regions and an optional file of regions to exclude from analysis.
Input format BAM+VCF
Output data A file containing haplotypes and MOI estimates for all combinations of three SNPs that fulfill the distance constraints, and a file contains a summary of final MOI estimates from a genome wide computation of haplotype counts.
Operating system Unix/Linux
Programming languages Perl
Computer skills Advanced
Stability Stable
Maintained Yes




No version available



  • person_outline Samuel Assefa

Publication for estMOI

estMOI citations


Molecular approaches to determine the multiplicity of Plasmodium infections

Malar J
PMCID: 5914063
PMID: 29685152
DOI: 10.1186/s12936-018-2322-5

[…] made., whole genome sequencing of field isolates is rapidly becoming common, and a number of software packages have been developed to identify multiclonal infections and reconstruct haplotypes. the estmoi software package can be used to analyse deep sequencing data for estimation of the presence of multiple genotypes, the number of infections, as well as proportions by phasing information […]


Large and finite sample properties of a maximum likelihood estimator for multiplicity of infection

PLoS One
PMCID: 5890990
PMID: 29630605
DOI: 10.1371/journal.pone.0194148

[…] possible moi of 5. an improvement, the real mccoil [] adapts a metropolis-hastings algorithm to estimate moi and minor-allele frequencies at uncorrelated snps in two different ways. the program estmoi [] requires deep sequencing data. the formal statistical framework in [] uses an em algorithm for snp data., here, we will further investigate the framework of [, ] and the concept of moi […]


Analysis of nuclear and organellar genomes of Plasmodium knowlesi in humans reveals ancient population structure and recent recombination among host specific subpopulations

PLoS Genet
PMCID: 5619863
PMID: 28922357
DOI: 10.1371/journal.pgen.1007008

[…] high quality snps after removing those in non-unique regions, and in low quality and coverage positions. samples were individually assessed for detecting multiplicity of infection (moi) using: (i) estmoi [] software, and (ii) quantifying the number of positions with mixed genotypes (if more than one allele at a specific position have been found in at least 20% of the reads []). the measures […]


Mapping sulphadoxine pyrimethamine resistant Plasmodium falciparum malaria in infected humans and in parasite populations in Africa

Sci Rep
PMCID: 5547055
PMID: 28785011
DOI: 10.1038/s41598-017-06708-9

[…] individuals, enabling quantification of parasites with different genotypes and distinguishing haplotypes in mixed infections, . whole genome data can be used to estimate moi, for example using the estmoi software. these techniques would provide extremely useful data but may not be available for routine surveillance of resistance markers for some time. the analyses presented in this paper show […]


Genomic variation in Plasmodium vivax malaria reveals regions under selective pressure

PLoS One
PMCID: 5426636
PMID: 28493919
DOI: 10.1371/journal.pone.0177134

[…] and oldest sample was used as ancestral haplotype. multiplicity of infection was estimated using a novel method of counting the unique haplotypes formed by polymorphism on paired sequencing reads (estmoi, []). for comparisons between populations, we first applied pca and neighbourhood joining tree clustering based on a matrix of pairwise identity by state values. these analyses were followed […]


Genomes of cryptic chimpanzee Plasmodium species reveal key evolutionary events leading to human malaria

Nat Commun
PMCID: 4804174
PMID: 27002652
DOI: 10.1038/ncomms11078

[…] variant, and appropriate cutoffs were selected to minimize false variant calls. using only snps from the core genome, the number of p. falciparum strains present in each sample was estimated using estmoi, with one likely mono-infection selected for each country (ers174561, bangladesh; ers050887, cambodia; ers347597, drc; ers010044, gambia; ers157479, ghana; ers042044, guinea; ers174601, laos, […]

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estMOI institution(s)
London School of Hygiene and Tropical Medicine, London, UK; Wellcome Trust Sanger Institute, Hinxton, UK; Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawia
estMOI funding source(s)
Supported by Medical Research Council UK, and Malaria Capacity Development Consortium funded by the Wellcome Trust.

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